Index - P

Page numbers followed by “f” indicate figures.

Page numbers followed by “t” indicate tables.

P bodies, 447, 457

P element, 243

P segments, 498

P16, 1164

p38 kinases, 746

p53, 907–908, 1020–1021, 1145, 1146, 1165–1166

P54 protein, 588, 588f

PABP. See Poly(A)-binding protein

PABPC. See Cytoplasmic poly(A)-binding protein

PABPC1. See Cytoplasmic poly(A)-binding protein

PAF. See Platelet-activating factor

PAGE. See Polyacrylamide gel electrophoresis

Pain receptors, 1062–1064

Palade, George Emil, 634

PALM. See Photo-activated localization microscopy

Palmitic acid, 51f

Palmitoyl CoA, 293, 295

Pancreas cells, 18f

Pancreatic β cells, 767, 767f

Pancreatic eIF2 kinase (PEK), 455

Paneth cells, 992, 994

Pannexins, 944

PAP. See Poly(A) polymerase

Pap smear, 1152

Papillae, 1064

Par proteins, 1006f

epithelial cell polarity and, 1007–1008, 1007f

nematode embryos and, 1003–1006

stem cells and, 1008, 1010, 1010f

Paracellular pathway, 941, 941f

Paracrine signaling, 675f, 676, 763

Paralogous sequences, 325

Parasites, 22, 24

eukaryotic, 1082

Parental types, 232

Parietal cells, 509–510, 509f

Parkin, 529

Parkinson’s disease, 87, 985f

Paroxetine, 1057

Passive immunization, 1089

I-25

Passive transport, 476

Patch clamps, 500–501, 500f, 501f

Pathogens, 1079

entry routes, 1081–1082

mechanical and chemical boundaries against, 1083–1084

replication sites, 1081–1082

Patterning genes, 26

Pax6 gene, 364, 365f, 366

Paxil, 1057

PC. See Phosphatidylcholine

PC3 endoproteases, 657

P-class pumps, 484, 484f, 488

PCNA. See Proliferating cell nuclear antigen

PCP. See Planar cell polarity

PCR. See Polymerase chain reaction

PD-1, 1131

PDE. See cGMP phosphodiesterase

PDE inhibitors, 716

PDGF. See Platelet-derived growth factor

PDI. See Protein disulfide isomerase

PD-L1, 1131

PDZ domains, 940

PE. See Phosphatidylethanolamine

Pectin, 969, 972

PEK. See Pancreatic eIF2 kinase

Pelizaeus-Merzbacher disease, 1045

Pemphigus vulgaris, 938

Penicillin, 137

Peptide bonds, 41, 69

planar, 81, 81f

synthesis of, 194

Peptide groups, 38f

planar, 81f

Peptide mass fingerprint, 118

Peptides

MHCs binding, 1107–1109, 1108f

phosphorylated, 684, 685f

Peptidoglycan, 47

Peptidyl-prolyl isomerases, 606

Peptidyltransferase reaction, 194

Perforins, 1086f, 1094, 1122–1123, 1123f

Pericentriolar material, 825

Peripheral membrane proteins, 284, 292

Peripheral nervous system, 1026, 1044, 1045f

Perlecan, 945, 950

Permissive temperature, 21, 228, 229f

Peroxisomal oxidation, 537, 538f

Peroxisomal proteins

import of, 620f

incorporation pathways, 620f, 621

targeting of, 619–621

Peroxisomal-targeting sequence 1 (PTS1), 619–621, 620f

Peroxisomes, 13f, 17

biogenesis and division, 621, 621f

fatty acid oxidation in, 537, 538f

Perutz, Max, 119

Pervasive transcription, 432–433

Petite mutations, 524, 525f

PH domain, 750

pH values, 55f

of biological fluids, 54–55, 54f

buffers and, 55–56, 56f

cytosolic, 485, 505–506

of endosomes, 662–663

enzyme activity dependent on, 95, 95f

in lysosomes, 489–491

in vacuoles, 489–491

Phages, 212

temperate, 216

Phagocytes, 1084

Phagocytosis, 16, 659, 776, 790–791

actin dynamics and, 792f

in apoptosis, 1012, 1012f

Phagosomes, 792f

Phalloidin, 792

Pharming, 561

Phase-contrast light microscopy, 140f, 141–142, 142f

Phenotype, 224

mutant allele effects on, 225f

of transcription factor mutations, 355f

Phenylalanine, 43

Pheromones, 673

Philadelphia chromosome, 1156, 1156f

Phosphatases, 103, 856

exit from mitosis and, 902

in signaling pathways, 676–677

Phosphate, 44

Phosphatidylcholine (PC), 49f, 277f

Phosphatidylethanolamine (PE), 277f

Phosphatidylinositol (PI), 277f, 282, 709, 710f

Phosphatidylinositol-3 kinase (PI-3 kinase), 749–750, 749f, 750f

Phosphatidylserine (PS), 277f, 282, 1015

Phosphoanhydride bonds, 61

Phosphodiester bonds, 41, 170, 170f

Phosphoenolpyruvate carboxylase, 577

Phosphofructokinase-1, 516–517

Phosphofructokinase-2, 517

Phosphoglycerides, 49, 49f, 50t, 276, 278

Phosphohistidine, 361

Phosphoinositide signaling pathways, 748–751

Phosphoinositides, 278, 748

Phospholipase A2, 290, 291f

Phospholipase C (PLC), 289, 692, 708, 710, 714, 749

second messengers from, 709–710, 710f, 712

Phospholipases, 282, 282f

Phospholipid anchors, 598–599

Phospholipid bilayers

biomembrane properties and composition of, 279

formation of, 273–274, 273f

gel and liquid phases of, 278–279, 279f

permeability of, 474, 474f

sealed compartment formed by, 274–276

Phospholipid molecules, 5f

Phospholipids, 9, 9f, 48–50, 49t

ABC proteins flipping, 493–494

annular, 287, 287f

fatty acid incorporation into, 294–295

flippases moving, 295

regulation of levels of, 763–766

synthesis and intracellular movement, 293–297, 294f

transport mechanisms, 296–297, 296f

Phosphoprotein phosphatase (PP), 703

Phosphoproteins, 103, 114, 1054

Phosphoproteomics, 124

Phosphoric acid, 56, 56f

Phosphorylated peptides, 684, 685f

Phosphorylated peptide-specific antibodies, 684

Phosphorylation, 103f

in Ca2+ ATPase, 487f

CDKs and, 883, 886

of lamins, 866

of MAP kinase family, 744–745, 744f

mRNP export and, 441–442, 442f

oxidative, 515

in protein regulation, 102–103

of rhodopsin, 697–698

of Smad transcription factors, 724

substrate-level, 516

Phosphotyrosine, 730, 731f

Phosphotyrosine phosphatases, 732–733, 733f

Photo-activated localization microscopy (PALM), 154f, 155

Photoelectron transport, 564–566, 564f

ROS protection in, 570

Photoinhibition, 570

Photomotility, 1046

Photophobia, 1046

Photophosphorylation, cyclic, 570–571

Photoreceptors, 740–741, 740f, 1061

Photorespiration, 576–578, 576f

Photosynthesis, 6, 62–63, 513, 514f, 560–566

ATP in, 563

CO2 metabolism during, 573–578, 575f

rates of, 564f

stages of, 561–563, 562f

Photosystem I (PSI), 563, 568, 569f

cyclic electron flow through, 570–571, 571f

regulation of, 571–572, 572f

Photosystem II (PSII), 563, 568, 569f

oxygen-evolving complex in, 569–570

regulation of, 571–572, 572f

Photosystems, 563–564

molecular analysis of, 567–572

proton-motive force in, 568–569

Phragmoplast, 860

PI. See Phosphatidylinositol

PI-3 kinase. See Phosphatidylinositol-3 kinase

PI-3 kinase pathway, 749–750

PIC. See Preinitiation complex

Piezo channels, 1063, 1064f

Piezo1, 1063, 1064f

Piezo2, 1063, 1064f

PINK1, 529

Pioneer transcription factors, 395–396

PKA. See Protein kinase A

PKB. See Protein kinase B

PKCs. See Protein kinase Cs

PKG. See Protein kinase G

PKR. See Protein kinase RNA-activated

Placental alkaline phosphatase (PLAP), 289

Plakins, 867

Planar cell polarity (PCP), 1008, 1009f

I-26

Planaria, 27–28, 988

Plant adhesion molecules, 971–972, 971f

Plant cell walls, 968–969, 968f

Plant cells, 4f

mitosis of, 860

stem cells, 996–999, 998f, 999f

Plant tissues, 968–972

Plant vacuoles, 17–18, 17f, 507

PLAP. See Placental alkaline phosphatase

Plaque assay, 213, 215f

Plaques, amyloid, 87, 88f

Plasma, 1082

Plasma cells, 1102

Plasma membrane, 9f, 13f, 271, 272f, 473

in bacteria, 10

depolarization of, 1034, 1035f

domains of, 657–658

electric potential across, 497, 498f

in myocardial infarction, 807

PI 3-phosphates in, 750

protein anchoring in, 289f

protein degradation, 665, 666f

protein sorting and, 657–658, 658f

retroviruses budding from, 666–667, 668f

store-operated Ca2+ channel, 713

targeting to, 585

Plasmalogens, 278

Plasma-membrane-attached protein signaling, 675f, 676

Plasmid cloning vectors, 236–237

Plasmid expression vectors, 251–253

gene and protein tagging, 252–253

retroviral systems, 252, 252f

transfection, 251–252

Plasmids, 10, 236

Plasmodesmata, 13f, 24, 969–970, 970f

Plasmodium falciparum, 22, 24, 525

Plasmodium species, 23f

Plastocyanin, 569

Platelet-activating factor (PAF), 966–967

Platelet-derived growth factor (PDGF), 685f, 686, 734, 813, 1159

Platelets, 964

PLC. See Phospholipase C

Pleated sheet, 71

Plectin, 867, 868f

PLP. See Proteolipid protein

Pluripotent cells, 976

Pluripotent stem cells, 988. See also Induced pluripotent stem cells

PML. See Promyelocytic leukemia

P-nucleotides, 1099

Podophyllotoxin, 830

Podosomes, 961

Point mutations, 204, 204f, 225, 1151

disease gene location and, 257

mRNA and, 257

Point-scanning confocal microscope, 147, 148f

Pol I. See RNA polymerase I

Pol II. See RNA polymerase II

Pol III. See RNA polymerase III

Pol β. See DNA polymerase β

Pol δ. See DNA polymerase δ

Pol ε. See DNA polymerase ε

Polar bonds, 34

Polar microtubules, 852

Polarity, 824

cell, 776, 776f, 1000–1010

cell division and, 1002–1003, 1002f

hyperpolarized state, 693

membrane depolarization, 1039–1040, 1042

plasma membrane depolarization, 1034, 1035f

Polarized cells, 931, 977

Polarized membrane traffic, 1003, 1007

Poliovirus, 1130

Polo kinase, 897, 916

Poly(A) polymerase (PAP), 180, 431, 452

Poly(A) sites, 303

Poly(A) tail, 180

Poly(A)-binding protein (PABP), 195, 196f, 431

in mRNP remodeling, 441, 441f

Polyacrylamide gel electrophoresis (PAGE), 108

kinase study with, 684

Polyacrylamide gels, 246

Polyadenylation

alternative, 450

cytoplasmic, 451–452, 452f

of pre-mRNAs, 430–432, 431f

3′ cleavage and, 419, 430–432, 431f

Polyclonal antibodies, 144

Polycomb proteins, 406–407, 408f, 409, 982

Polycystic kidney disease, autosomal dominant, 849

Polydactyly, 354

Polygenic diseases, 258

Polyglutamine, 311

Polyglutamylation, 843, 843f

Polyglycylation, 843, 843f

Poly-K63 ubiquitin-binding domain, 760

Polylinkers, 237

Polymerase chain reaction (PCR), 234, 239–243, 241f

gene sequencing and, 243–244, 244f, 245f

isolation of specific segments of DNA, 241–242, 242f

Polymers, 6, 41, 169

Polypeptides, 70

binding to ER, 589

chaperonins and folding, 85, 86f

in ER, 590–591

MHC molecules binding to, 1108–1109

structure of, 69f

synthesizing chains of, 194

translocon allowing passage of, 590, 590f

Polyploid organisms, 224

Polyribosomes, 195

Polysaccharides, 7, 41, 46–48

Polysomes, 195

Polyspermy, 979

Polytene chromosomes, 343–345, 345f

Polytenization, 344

Polyubiquitiny chains, 760

Polyubiquitinylation, 103, 104f

Polyunsaturated fatty acids, 49

Porins, 288, 288f, 523

Positive feedback mechanisms, 876

intrinsic polarity program and, 1000–1002, 1001f

Postmitotic cells, 876

Postsynaptic cell dendrites, 1028

Postsynaptic density (PSD), 1050

Postsynaptic target cells, 1048

Post-transcriptional gene control, 418f, 419

cytoplasmic mechanisms, 445–460

Post-translational translocation, 591–592, 592f

Potential energy, 57

Power stroke

dynein, 839f

myosins, 800, 801f

PP. See Phosphoprotein phosphatase

PP1. See Protein phosphatase 1

PP2A. See Protein phosphatase 2A

PPARγ, 770, 771f

PRC1 complex, 407, 408f

PRC2 complex, 407, 408f, 982

Pre-B cells, 1100

Pre-B-cell receptor, 1100–1101, 1101f

Precancerous polyps, 1153

Precursor cells, 988

Precursor mRNAs (pre-mRNAs), 180–181, 181f, 417, 420t

nuclear exoribonucleases degrading, 432

processing of eukaryotic, 419–433

proteins associating with, 421–422

regulation of processing, 435–440

snRNAs base pairing with, 424, 425f, 426

spliceosome and, 426–427, 443

SR proteins and exon definition in, 428–429, 429f

3′ cleavage and polyadenylation of, 430–432, 431f

Precursor rRNA (pre-rRNA), 367, 420t

nucleolar organization and, 461–462, 462f

processing of, 462–465, 464f

transcription units, 462, 462f

Precursor tRNA (pre-tRNA), 420t

modification in nucleus, 466–468

processing of, 467, 467f

Preinitiation complex (PIC), 191, 192f, 374, 375f, 376f

pre-mRNAs. See Precursor mRNAs

pre-mRNPs, 419

Prenyl anchors, 289

Prenylation, 288

Preprophase band, 860

pre-rRNA. See Precursor rRNA

Pre-rRNA genes, 461–462

Presenilin 1 (PS1), 762

Presynaptic neurons, 1048, 1049–1050

Presynaptic terminal, 1054

pre-tRNA. See Precursor tRNA

Primary cell cultures, 131–132

Primary cell walls, 969

Primary cilium, 757, 847–848, 848f

defects in, 848–849

Primary electron acceptor, 563

Primary lymphoid organs, 1082

Primary structure, 70

I-27

Primary transcripts, 417

Primase, 199

Primer, 198, 200f

Prions, 87

Pro-apoptotic proteins, 1018

Procaspases, 1015, 1018, 1126

Processed pseudogenes, 321

Procollagen molecules, 951

Proenzymes, 656

Professional APCs, 1105–1106

Profilin, 784–785

Progenitor cells, 988

Progeria, 866

Progesterone, 879, 879f, 1157

Programmed cell death, 906, 977, 1011, 1011f, 1012–1013, 1012f

Prohormone, 104

Proinsulin, 656f

Projection neurons, 1067

Prokaryotic cells

DNA transposons in, 314, 315f

gene organization, 179, 180f

structure and function of, 10–12, 10f

Prolactin, 727

Proliferating cell nuclear antigen (PCNA), 200

Proline, 44

Proline isomerases, 86, 87f

Prometaphase, 851, 853–854, 855f

Promoter fusion, 253

Promoter-proximal elements, 378–379

Promoters, 176, 364, 731

experimentally regulated, 260–261

RNA polymerase II, 371–373

Promyelocytic leukemia (PML), 469

Promyelocytic leukemia nuclear bodies, 469

Proofreading, 188, 203, 204f, 528, 528f

Prophage, 216

Prophase, 850, 875

Proprioceptive neurons, 1017, 1017f

Proproteins, 656

Prostaglandin E1, 701

Prostate cancer, 1155

Prosthetic groups, 95, 540, 540t

Proteases, 76

ADAM and, 763

metalloproteases, 960

MMP, 761, 763, 960

serine, 92–96, 94f

Proteasome, 97–99, 98f

immunoproteasome, 1111

ubiquitin and, 99–100

Proteasome inhibitors, 99

Protein binding, 89–96

ligands in, 89, 90f

Protein cleavage-controlled signaling pathways, 761–766

Protein coats, 638–639

Protein Data Bank, 119, 121

Protein degradation, 97

plasma membrane, 665, 666f

proteasome and, 97–99

signaling pathways controlled by, 751–760

ubiquitin and, 99–100

Protein disulfide isomerase (PDI), 603–604, 604f

Protein expression profiling, 122

Protein family, 306

Protein folding, 81–89, 82f

abnormal, 87, 88f

amino acid sequence and, 81–82

catalysts in, 606–607

chaperone-mediated, 83–85, 84f, 604–606, 605f

chaperones promoting, 82–86

chaperonin-mediated, 85–86, 86f

in ER, 601–608

ER proteins and, 604–606, 605f

improper, 606–607

isomerizations and, 606

oil drop model for, 72, 73f

planar peptide bonds and, 81, 81f

proline isomerases promoting, 86, 87f

Protein fusion, 253

Protein kinase A (PKA), 679

activation of, 701–702, 702f, 703–704

anchoring proteins localizing, 705–706, 706f

cell types and activation of, 703–704, 704t

gene transcription and, 704–705, 705f

glycogen metabolism regulation by, 702–703, 703f

signal amplification and, 704

signal suppression, 706–707

structure of, 702f

Protein kinase B (PKB), 748, 750–751, 750f, 767, 1019f

Protein kinase Cs (PKCs), 709, 714, 748

Protein kinase G (PKG), 714–716, 715f

Protein kinase RNA-activated (PKR), 455

Protein kinases, 874. See also specific protein kinases

in signaling pathways, 676–677

Protein modification, in ER, 601–608

Protein phosphatase 1 (PP1), 899

Protein phosphatase 2A (PP2A), 900, 916

Protein phosphatases, in signaling pathways, 676–677

Protein regulation, 97–105

allosteric, 100–101

high-order, 105

phosphorylation and dephosphorylation in, 102–103, 103f

proteolytic cleavage in, 104–105

ubiquitinylation and deubiquitinylation in, 103–104

Protein self-splicing, 105

Protein sorting, 583

pathways for, 583–584, 584f

plasma membrane and, 657–658, 658f

trans-Golgi and, 657–658, 658f

Protein structure

categories of, 72–73

comparing, 79–80

determining, 118

function and, 68f

hierarchical, 69–80

motifs, 75–76, 76f, 325

primary, 69–70

quaternary, 78

secondary, 70–71, 71f, 72f

tertiary, 72

Protein synthesis

AUG start codon in, 190–191

cell-free, 587, 587f

chain elongation, 193–195, 193f

completion of, 195

global regulation of, 452–455

GTPase superfamily role in, 195–196

microsomes and, 587–588, 587f

nonsense mutations and, 196–197

ribosomes and, 188–197

RNA roles, 183, 183f

secretory proteins, 587, 588–589, 589f

translation efficiency, 195, 196f

translation initiation, 191, 192f, 193

translation termination, 194f, 195

Protein targeting, 583

to endoplasmic reticulum, 585–592

to lysosomes, 653–655, 653f

to mitochondria and chloroplasts, 608–617

Protein transport

assaying, through secretory pathway, 634–635, 635f

COPI vesicle-mediated, 647–648

COPII vesicle-mediated, 645–647

from trans-Golgi, 651–652

Protein-coding genes, 305–307

number of, in genome, 326–327, 326f

transcription of, 176–182

Protein-folding catalysts, 606–607

Proteins, 2, 7f, 41. See also specific proteins

accessory, 805

alternative RNA splicing and, 181–182

amino acids in formation of, 7, 42–45, 43f

anchoring, 705–706

biomembrane, 284–292

bonding, 40, 40f

cell cycle, 21–22

in cell structure and tasks, 7

chimeric, 130, 612–613, 612f

cholesterol and sphingolipids clustering with, 282–283

cognate, 380

cross-linking, 793, 794f

cytoskeletal, 7

cytosolic, 99–100

delivery of, 583

depicting conformation of, 74–75, 75f

determining conformation, 119, 120f, 121

DNA interaction with, 172, 172f

in DNA replication, 199–201

domains, 76–78

double mutants in studying function order, 230–231

enzyme and antibody assays detecting, 111–114, 113f

evolutionary relationships among, 325

fluorescent, 146–147, 146f

functions of, 68

GPI-anchored, 599, 599f

I-28

GTP-hydrolyzing, 588–589

homology among, 80

integral membrane, 72–74, 284, 292

interacting, 231–232, 232f

lipid-anchored membrane, 284, 288–289

liquid chromatography of, 109–111

mass spectrometry of, 116, 116f, 117f, 119

membrane interaction with, 284–285

membrane transport, 68

misfolded, 87, 88f

motor, 68

multimeric membrane, 287, 287f, 601

order of functioning of, 230–231, 231f

peripheral membrane, 284

production from cloned genes, 250–251, 250f

purifying, detecting, and characterizing, 105–121

redundant, 231–232, 232f

regulation of activity of, 677, 677f

regulation of concentrations of, 354, 354f

regulation of transcription and replication, 339

regulatory, 68

removal from membranes, 290–292, 291f, 292f

scaffold, 67, 805

sequence comparison, 79–80

signaling, 68

stabilizing, 805

stepwise synthesis on ribosomes, 188–197

tail-anchored, 597

transmembrane, 285–287, 285f, 286f, 289–290

Proteoglycans, 723, 925, 945, 950, 951, 953–956

aggregate, 956, 957f

diversity of, 955–956

Proteolipid protein (PLP), 1044

Proteolysis, 98f, 1111, 1113–1114

Proteolytic cleavage, 104–105, 656f

Proteolytic processing, 656–657, 657f

Proteomics, 122–124

mass spectrometry in, 123–124, 123f, 124f

of organelles, 164

Protofibril, 861

Protofilaments, 823–824, 828, 861

Proton pumping, 539–540, 540f, 542–546

stoichiometry of, 549–550

Proton translocation, 556

Proton-motive force, 514, 515f, 539, 550, 613

ATP synthesis and, 551–559

ATP-ADP exchange and, 556, 558, 558f

heat generation with, 558–559

in mitochondria, 550

photosystem electron flow generating, 568–569

Proton/sucrose antiporter, 507, 507f

Proto-oncogenes, 1135, 1150t, 1161

apoptosis regulation genes as, 1163

gain-of-function mutations converting, 1149, 1151

MYC, 1145

viruses activating, 1152

Protostomes, 26

Protozoans, 22, 23f, 24

splicing in, 428

Provirus, 217, 444

Prozac, 1057

PS1. See Presenilin 1

PSD. See Postsynaptic density

PSD95, 1051, 1051f

Pseudogenes, 307

processed, 321

Pseudomonas fluorescens, 215f

Pseudosubstrate domain, 701

PSI. See Photosystem I

PSII. See Photosystem II

Psoriasis, 681

PTEN gene, 751, 1163

PTEN phosphatase, 751, 1156

PTS1. See Peroxisomal-targeting sequence 1

Pull-down assays, 685f, 686

Pulse-chase experiments, 115, 115f, 586, 661f

Puma, 1019f, 1020–1021

Pumps, 476

ATP-powered, 475f, 476, 483–494, 484f

Ca2+, 486–489

electrogenic, 490

F-class, 484f, 485

K+, 476f

Na+K+, 476, 476f, 486

P-class, 484, 484f, 488

regulation of, 489

V-class, 484f, 485, 489–491, 491f, 510, 510f

Purines, 45, 46f

Purkinje neurons, 4f, 1071f

Purple bacteria, 567, 568f

P-values, 324

Pyranoses, 47

Pyrimidines, 45, 46f, 170

Pyrophosphate, 46

Pyruvate, 518, 519f, 533

Pyruvate dehydrogenase, 533

Pyruvate kinase, 516